Constructing Metabolic Models

KBase has a suite of Apps and data that support the reconstruction, prediction, and design of metabolic models in microbes and plants. Genome-scale metabolic models are primarily reconstructed from protein functional annotations. These genome-scale metabolic models can be used to explore an organism’s growth in specific media conditions, determine which biochemical pathways are present, optimize production of an important metabolite, identify high flux pathways, and more.

Metabolic models can be used to evaluate an organism’s metabolic capability by simulating growth under different conditions to answer important biological questions such as:

  • What biochemical pathways are present?

  • What are the high flux pathways under a certain growth condition?

  • Could the organism grow anaerobically?

  • Would it grow under certain minimal media conditions?

  • Could the organism be optimized to produce a particular drug molecule or industrially important biofuel?

Flowchart of Apps used in Metabolic Modeling.

Learn More

The flowchart above shows KBase’s metabolic modeling tools (green) as well as some other analysis tools. Check the App Catalog for the latest set of metabolic modeling analysis tools (Apps).

The video tutorial below presents an introduction to building metabolic models in KBase. The “Microbial Metabolic Model Reconstruction and Analysis” Narrative tutorial lets you see and try out for yourself some examples of KBase’s metabolic modeling functionality in action. Common questions and answers about KBase’s metabolic modeling tools can be found in the Metabolic Modeling FAQ.

Video Tutorial

Narrative Tutorial

Microbial Metabolic Model Reconstruction and Analysis Tutorial – guides through a workflow on how to draft a metabolic model and use KBase Apps to gapfill, run flux balance analysis and simulate growth.